Transcript MIKADO tool - OceanDNA

3rd SeaDataNet training course – Ostende – 16-19 June 2008
OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
MIKADO tool
M. Fichaut, V. Tosello, M. Larour
www.seadatanet.org
OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Overview
• Objectives, background and technical characteristics
• Mikado main features
• Differences between MIKADO V0 and V1
• Manual input of metadata
• Use of the common SDN vocabularies
• Automatic XML generation
• Connection to the local database
• Query writing
• Mapping to the local database
• Practical work session
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Objective
 MIKADO is used to generate XML catalogue descriptions, it
creates XML ISO-19115 files using SDN common
vocabularies for metadata exchange of





CSR - Cruise Summary Reports
EDMED - Marine Environmental Data sets
CDI - Common Data Index
EDMERP - Marine Environmental Research Projects
[EDIOS – Permanent Ocean-observing System]
 To use MIKADO you must be familiar with the XML
documentation of SDN which can be downloaded from
BSCW :
www.seadatanet.org
SDN Technical Task Team
ISO
Application of ISO 19115 within SeaDataNet V1
XML METADATA for CSR V1 ….
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Some background
• Mikado version 0
• created for the SEA-SEARCH project
• used for SeaDataNet V0
• Mikado version 1
• New version of Mikado to be compliant with the
SeaDataNet V1 XML schemas, and the SeaDataNet
common vocabularies
• Completely rewritten, more user friendly
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Technical characteristics
• Written in Java Language (Version >= 1.6)
• Available under multiple environments :
• Microsoft : Windows 2000, XP, VISTA
• APPLE
• Unix - Solaris
• Linux
• Use of the SeaDataNet common vocabularies web services
• to update lists of values of the SeaDataNet common vocabularies
• need network connections in order to have up to date lists of
values.
• But Mikado works offline once the list are up-to-date
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO main features (1)
MIKADO can be used in 2 different ways
• One manual way, to input manually information for the
catalogues and CDI in order to generate XML files.
• One automatic way, to generate XML descriptions
automatically, from information catalogued in a relational
database. Automatic way is needed for those who have
many entries referenced in a relational database
Only one interface for all catalogues
• Same look
• Same principles
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO main features (2)
Manual
MIKADO
Java code
Automati
c
XML files
for SeaDataNet
catalogues
CSR
EDMED
EDMERP
CDI
[EDIOS]
DATABASE
JDBC
Java DataBase Connectivity
Native Drivers
MYSQL
ORACLE
POSTGRES
SQLServer
www.seadatanet.org
Bridge Drivers
using Microsoft ODBC
EXCEL File
(ACCESS, EXCEL, SQL SERVER)
Other Drivers
Downloaded from ad hoc Websites
(Copied in the dist/lib MIKADO directory)
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Differences between V0 and V1
• No need to modify configuration files with JDBC connections and SQL
queries
• database connection and the user the queries are save as XML
files
• EDMERP catalogue available in MIKADO
• Manual Input of data
• Input screens updated to be compliant with the new XML schemas
• List of values = common vocabularies
• Automatic generation of XML files : more interactive and user-friendly
• Help for JDBC connection – connection checking
• Help for the SQL query writing – query checking and query saving
• Incremental mapping with the local database
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO – Manual input
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO – Manual input
• Available for 4 catalogues : EDMED, CSR, CDI, EDMERP
• EDIOS will be also available in the near future
• Each input generates an XML file that can be sent to the
central catalogues
• For EDMERP and CSR : EDMERP CMS and CSR online can
also be used, but MIKADO is useful
• if you have problems with the NETWORK connection
• if you want to keep locally an XML description of your
catalogues
• For EDMED and CDI, there is no online input tools.
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO and vocabulary lists
List
code
List Name
List
code
List Name
C16
SeaDataNet Sea Areas
L061
SeaDataNet Platform Classes
C77
ICES ROSCOP data types
L081
SeaDataNet Data Access Restriction Policies
C174
SeaDataNet CSR ship metadata
L101
SeaDataNet geographic co-ordinate reference frames
C320
ISO countries
L111
Height and Depth Vertical Co-ordinate Reference Datum
C371
Ten-degree Marsden Squares
L181
ROSCOP sample quantification units
C381
Ports Gazetteer
L231
SeaDataNet metadata entities
L05
SeaDataNet device categories
L241
SeaDataNet data transport formats
L021
SeaDataNet Geospatial Feature Types
P021
BODC Parameter Discovery Vocabulary
L031
SeaDataNet Measurement Periodicity Classes
P081
SeaDataNet Parameter Disciplines
EDMERP
European marine projects
EDMO
European marine organisation
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO and vocabulary lists
•Automatic check of the
version of the vocabulary lists :
once when MIKADO starts
• MIKADO downloads locally
the latest version of each list
•Possible to enable-disable the
automatic check and download
of the lists and to work offline
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO manual – vocabulary lists (1)
Common vocabulary BODC,
list C320 (Country ISO codes)
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO manual – vocabulary lists (2)
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO – Automatic XML generation
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - connexion
• Help for the
connexion to
the database
• Pre-filled
information for
some
databases
• Check the
connexion
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – connexion OK
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO – automatic – connexion KO
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – queries
Expendable tree
• Main query
Return the ID
• Single queries
Return 1 row
• Multiple queries
Return 1 to n rows
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – queries
Write the queries
• SQL syntax (for Oracle,
Excel, MySQL, …) and
SQL variables must be
adapted to your own data
base
Check the Queries
• Green OK
• Red KO : read the error
message
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – single queries
All the XML variables
are listed in the
expendable tree
• In bold : mandatory
fields
• 1 to n single subquery
can be written
• In green : fields already
fulfilled
• Add or to detele
variables in a query
• Check the query
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – multiple queries
All the XML variables
are listed in the
expendable tree
• Number of queries is
pre-defined
• The list of variables for
each of these multiple
queries is also predefined
• In bold : mandatory
field
• In green : fields already
fulfilled
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic – multiple queries
• In a group of
variables
(same XML
block, same
pre-defined set
of variable in a
query), the non
mandatory
variables can
be left to null
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - Save the queries
When all the
queries are
written
• They can be
saved in an
XML file to
be re-used
later on
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - generate the XML files
1. Select the
catalogue you want
to generate
2. Open the
corresponding
queries
3. Choose the output
directory
4. Export the XML files
•
Progress bar
•
Cancel allowed
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - local mapping
While generating the XML files for all the catalogues
• Each time that MIKADO does not recognized a value
(entrykey or entryterm) which should come from the common
vocabulary, it asks the user for mapping
• MIKADO manages a demand-driven continuous (incremental)
extension of a local mapping : mapping of the local database
to the common vocabulary
• Mapping tables can be modified
• Delete rows
• Modify the LOCAL value
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - local mapping
Example
CSR
generation
• Mapping of
the platform
type
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO automatic - local mapping
Modification of
the local
mapping
If wrong entries
have been input,
it is possible to:
• Delete one entry
• Delete all the
entries
• Change the local
code
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO – User manual
User manual is provided :
in : SDN_tools\Mikado_usermanual
File : SDN_MIKADO_UserManual_v1.pdf
• Detailed explanations for MIKADO use, lots of
snapshots
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 MIKADO helpdesk
When using MIKADO
• Questions and errors must be reported to
[email protected]
• Subject of the mail should be :
• MIKADO question or
• MIKADO error
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Practical work – to-morrow
• Manual input of one EDMED form
• Manual input of one Cruise Summary Report
• Automatic generation of CDI files
• One dataset of 81 XBT SIPPICAN files
• EXCEL or MySQL
• Use the XML validator to see if your files are valid
• Copy MIKADO material on your own computer
• Copy the directory SDN_TOOLS.zip file and unzip it
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Practical work – requirements
Make sure that the java version is > = 1.6
1) To know if Java is available on your computer, in the right
version, follow these steps :
- Open 'Start' menu, then 'Execute'
- On the displayed window, enter: 'cmd', then click on 'OK'
button
- Enter 'java -version'
2) Check if command has been executed :
- If not, download the last java version at
http://java.com/en/download/index.jsp.
- Else, check the version displayed.
The version should be greater than or equal to 1.6.
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
 Practical work – requirements
For the trainees who want to test Mikado with MySQL
•
Those who have already MySQL on their labtops : make sure that
MySQL Query Browser is also available.
• If not, you must install it by double clicking on the following file
from the common directory
SDN_tools\databases\mysql\install\Query_browser\
file : mysql-gui-tools-5.0-r12-win32.msi
• Those who do not have MySQL: let us know, we will install it on your
notebook.
www.seadatanet.org
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OBSERVATIONS
& PRÉVISIONS CÔTIÈRES
3rd SeaDataNet training course – Ostende – 16-19 June 2008
ANY QUESTIONS?
www.seadatanet.org
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